Variant report

Variant	rs73825138
Chromosome Location	chr3:28388922-28388923
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr3:28388660-28391432	K562	blood:	n/a	n/a
2	CHD2	chr3:28388827-28389500	Hela-S3	cervix:	n/a	n/a
3	EP300	chr3:28388598-28389510	Hela-S3	cervix:	n/a	chr3:28389265-28389279
4	ARID3A	chr3:28388520-28389643	K562	blood:	n/a	n/a
5	IRF1	chr3:28388625-28391554	K562	blood:	n/a	chr3:28391536-28391549 chr3:28391382-28391398
6	GTF2F1	chr3:28388831-28391464	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr3:28388873-28392054	IMR90	lung:	n/a	n/a
8	POLR2A	chr3:28388560-28395839	MCF10A-Er-Src	breast:	n/a	n/a
9	RCOR1	chr3:28388902-28391338	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr3:28388762-28392516	K562	blood:	n/a	n/a
11	POLR2A	chr3:28387839-28396035	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr3:28388480-28391466	Hela-S3	cervix:	n/a	chr3:28389286-28389299 chr3:28389338-28389351 chr3:28389338-28389351 chr3:28389223-28389236 chr3:28389287-28389298 chr3:28389286-28389297
13	HCFC1	chr3:28388191-28391638	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:28388916-28391389	Hela-S3	cervix:	n/a	n/a
15	TEAD4	chr3:28388863-28391561	K562	blood:	n/a	n/a
16	TBP	chr3:28388807-28391345	Hela-S3	cervix:	n/a	n/a
17	IRF1	chr3:28388035-28391677	K562	blood:	n/a	chr3:28391536-28391549 chr3:28391382-28391398

No.	Distal block	Cell Line	Cell type
1	chr3:28279814..28285757-chr3:28388127..28392208,14	K562	blood:
2	chr3:28370043..28372109-chr3:28386223..28389083,2	MCF-7	breast:
3	chr3:25703874..25707156-chr3:28388631..28391167,3	K562	blood:
4	chr3:28355500..28357413-chr3:28388215..28391040,2	MCF-7	breast:
5	chr3:28388905..28390597-chr6:26234908..26237633,2	K562	blood:
6	chr3:28279814..28284603-chr3:28388127..28392296,9	K562	blood:
7	chr3:28373806..28377718-chr3:28387703..28390768,4	MCF-7	breast:
8	chr3:25703874..25706780-chr3:28388631..28390300,2	K562	blood:

Variant related genes	Relation type
ZCWPW2	TF binding region
ENSG00000187118	Chromatin interaction
ENSG00000124575	Chromatin interaction
ENSG00000264219	Chromatin interaction
ENSG00000163512	Chromatin interaction
ENSG00000077097	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11916224	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11918809	0.83[AMR][1000 genomes]
rs11919446	1.00[EUR][1000 genomes]
rs11923033	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11923748	1.00[EUR][1000 genomes]
rs11926821	1.00[EUR][1000 genomes]
rs55758484	1.00[EUR][1000 genomes]
rs55817728	1.00[EUR][1000 genomes]
rs55962685	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs56082224	1.00[EUR][1000 genomes]
rs56199335	1.00[EUR][1000 genomes]
rs57400334	1.00[EUR][1000 genomes]
rs57850842	1.00[EUR][1000 genomes]
rs60023459	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60355399	1.00[EUR][1000 genomes]
rs61588415	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6794482	1.00[EUR][1000 genomes]
rs6800120	1.00[EUR][1000 genomes]
rs6800367	1.00[EUR][1000 genomes]
rs6804419	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73822335	0.83[AMR][1000 genomes]
rs73822569	0.85[AMR][1000 genomes]
rs73822571	0.85[AMR][1000 genomes]
rs73822575	0.85[AMR][1000 genomes]
rs73822579	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73822639	1.00[EUR][1000 genomes]
rs73822644	1.00[EUR][1000 genomes]
rs73822646	1.00[EUR][1000 genomes]
rs73822647	1.00[EUR][1000 genomes]
rs73823977	1.00[EUR][1000 genomes]
rs73823978	1.00[EUR][1000 genomes]
rs73823979	1.00[EUR][1000 genomes]
rs73823980	1.00[EUR][1000 genomes]
rs73823981	1.00[EUR][1000 genomes]
rs73823982	1.00[EUR][1000 genomes]
rs73823983	1.00[EUR][1000 genomes]
rs73823984	1.00[EUR][1000 genomes]
rs73823985	1.00[EUR][1000 genomes]
rs73823986	1.00[EUR][1000 genomes]
rs73823988	1.00[EUR][1000 genomes]
rs73825125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73825141	0.90[AFR][1000 genomes]
rs73825145	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73825155	1.00[EUR][1000 genomes]
rs73825158	1.00[EUR][1000 genomes]
rs73825159	1.00[EUR][1000 genomes]
rs73825160	1.00[EUR][1000 genomes]
rs73825164	1.00[EUR][1000 genomes]
rs7627778	1.00[EUR][1000 genomes]
rs7628073	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7649677	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
2	chr3:28349800-28389400	Weak transcription	Gastric	stomach
3	chr3:28358800-28389000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:28363600-28389000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:28363800-28389600	Weak transcription	Spleen	Spleen
6	chr3:28365400-28389400	Weak transcription	Lung	lung
7	chr3:28366200-28389400	Weak transcription	Colonic Mucosa	Colon
8	chr3:28366400-28389200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:28367000-28389000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:28367200-28389400	Weak transcription	Pancreas	Pancrea
11	chr3:28377800-28389200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr3:28378400-28389400	Weak transcription	Ovary	ovary
13	chr3:28379000-28389600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:28380600-28389200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:28380800-28389200	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:28381600-28389200	Weak transcription	Placenta	Placenta
17	chr3:28383800-28389400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr3:28384000-28389200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:28385800-28389200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr3:28386000-28389200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:28386400-28389000	Enhancers	Brain Anterior Caudate	brain
22	chr3:28386400-28389000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr3:28386400-28389400	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr3:28387000-28389000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr3:28387000-28389400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr3:28387200-28389200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr3:28387400-28389200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:28387400-28389600	Flanking Active TSS	Dnd41	blood
29	chr3:28387600-28389000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr3:28387600-28389000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr3:28387600-28389400	Enhancers	Placenta Amnion	Placenta Amnion
32	chr3:28387600-28389600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr3:28387600-28391600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:28387600-28392200	Active TSS	Right Atrium	heart
35	chr3:28387800-28389000	Enhancers	Primary B cells from cord blood	blood
36	chr3:28387800-28389000	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr3:28387800-28389000	Enhancers	HUVEC	blood vessel
38	chr3:28387800-28389200	Enhancers	Fetal Intestine Small	intestine
39	chr3:28387800-28389400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:28387800-28389400	Active TSS	Fetal Brain Male	brain
41	chr3:28387800-28389400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr3:28388000-28391600	Active TSS	Psoas Muscle	Psoas
43	chr3:28388000-28392000	Active TSS	NHLF	lung
44	chr3:28388200-28389000	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr3:28388200-28389400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:28388200-28389400	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr3:28388200-28391400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:28388200-28391400	Active TSS	Right Ventricle	heart
49	chr3:28388200-28391800	Active TSS	HMEC	breast
50	chr3:28388200-28392000	Active TSS	GM12878-XiMat	blood

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